Align alcohol dehydrogenase (EC 1.1.1.1); all-trans-retinol dehydrogenase (NAD+) (EC 1.1.1.105) (characterized)
to candidate PfGW456L13_3630 S-(hydroxymethyl)glutathione dehydrogenase (EC 1.1.1.284)
Query= BRENDA::C7R702 (374 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3630 Length = 372 Score = 619 bits (1596), Expect = 0.0 Identities = 296/370 (80%), Positives = 337/370 (91%) Query: 5 VIKCKAAVAWEAGKPLSIEEVEVQPPQKGEVRVKIVATGVCHTDAFTLSGDDPEGVFPSI 64 +IK +AAVA+ A +PL I EV+V PPQ GEV V+IVATGVCHTDAFTLSG DPEG+FP I Sbjct: 1 MIKSRAAVAFAANQPLQIVEVDVAPPQAGEVLVRIVATGVCHTDAFTLSGADPEGIFPVI 60 Query: 65 LGHEGGGIVESVGEGVTSVKPGDHVIPLYTPECGDCKFCLSGKTNLCQKIRETQGKGLMP 124 LGHEGGGIVE+VGEGVTS+ GDHVIPLYTPECG+CKFC SGKTNLCQKIR TQGKGLMP Sbjct: 61 LGHEGGGIVEAVGEGVTSLAVGDHVIPLYTPECGECKFCTSGKTNLCQKIRATQGKGLMP 120 Query: 125 DGTTRFSINGKPIYHYMGTSTFSEYTVLPEISLAKVNPKAPLEEVCLLGCGVTTGMGAVM 184 DGT+RFS G+P++HYMGTSTFSEYTVLPEISLAK+ APLE+VCLLGCGVTTG+GAV+ Sbjct: 121 DGTSRFSYEGQPVFHYMGTSTFSEYTVLPEISLAKIPKDAPLEKVCLLGCGVTTGIGAVI 180 Query: 185 NTAKVEEGATVAIFGLGGIGLSAVIGAVMAKASRIIAIDINESKFELAKKLGATDCVNPK 244 NTAKVEEGA+VAIFGLGGIGL+A+IGA MAKA RIIAIDIN +KFE+A++LGATD +NPK Sbjct: 181 NTAKVEEGASVAIFGLGGIGLAAIIGATMAKAGRIIAIDINPAKFEIARQLGATDFINPK 240 Query: 245 DYDKPIQEVIVEMTDGGVDYSFECIGNVNVMRSALECCHKGWGESVIIGVAGAGQEISTR 304 DYD+PIQ+VI+EMT+GGVDYSFECIGNV++MR+ALECCHKGWGESVIIGVAGAGQEISTR Sbjct: 241 DYDRPIQDVIIEMTEGGVDYSFECIGNVHLMRAALECCHKGWGESVIIGVAGAGQEISTR 300 Query: 305 PFQLVTGRVWKGTAFGGVKGRSELPDYVERYLAGEFKLDDFITHTMPLEKINDAFDLMHE 364 PFQLVTGRVW+G+AFGGVKGRSELP YVE G+ LD FITHTM LE+IN AFDLMH+ Sbjct: 301 PFQLVTGRVWRGSAFGGVKGRSELPSYVENAQKGDIPLDSFITHTMGLEEINRAFDLMHK 360 Query: 365 GKSIRSVIHY 374 G+SIR+VIH+ Sbjct: 361 GESIRTVIHF 370 Lambda K H 0.317 0.137 0.413 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 595 Number of extensions: 19 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 374 Length of database: 372 Length adjustment: 30 Effective length of query: 344 Effective length of database: 342 Effective search space: 117648 Effective search space used: 117648 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory